Recently, scientists introduced a new type of microscope capable of investigating nonconducting surfaces in an atomic scale, which is called AFM (Atomic Force Microscope). It was an innovative attempt to overcome the limitation of STM (Scanning Tunnelling Microscope) which has been able to obtain the image of conducting surfaces. Surfaces of samples are imaged with atomic resolution. The AFM is an imaging tool or a profiler with unprecedented 3-D resolution for various surface types. The AFM technology, however, leaves a lot of room for improvement due to its delicate and fragile probing mechanism. One of the room for improvements is gap control between probe tip and sample surface. Distance between probe tip and sample surface must be kept in below one Angtrom in order to measure the sample surface in Angstrom resolution. In this paper, AFM system modeling, experimental system identification and control scheme based on system identification are performed and finally sample surface is measured by home-built AFM with such a control scheme.